Advice on Encoding Audio for Dolby 5.1

Hi: I am attempting my first DVD SP project with 5.1 audio. I have a few questions that I was hoping someone could help me with.
I understand enough to use Compressor to create .m2v and .ac3 files for import into DVD SP. I also understand how to set Audio Coding Mode in the Inspector to: 3/2 (L,C,R,Ls,Rs) with LFE enabled.
I am starting from a large Quicktime file with 12 tracks, of which 10 are audio tracks (including the Music and Effects tracks).
I would like to create an option for the viewer to select Stereo or 5.1 surround. I understand that I can encode the audio twice: once for stereo and once for 5.1, and that I can assign the appropriate audio stream to the button when I build the menu.
But here is my question: do I need to extract the 6 audio tracks from the quicktime and encode them separately, or is Compressor smart enough to select the correct tracks depending on the options I choose in the Inspector prior to encoding?
I hope that makes sense. Thank you in advance for any assistance.

The answer to this question is yes: I extracted the six tracks separately from the quicktime file also including the timecode track with each extraction.
After saving the six separate files - LT, RT, Center, LFE, Rs and Ls - choose the "Add Surround" option and assign the tracks accordingly. Compressor has an audio preset for encoding these files into on AC3 file.

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